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Optimise alignment/final alignment computation master

Open rrahn opened this issue 5 years ago • 3 comments

This PR enables the logging mechanism for the new alignment algorithm implementation.

The logging policy is only available if the alignment runs in debug modus. In this case special functions are available to log the matrix and later to transfer the matrix to the computed alignment result. Since policies cannot easily communicate with each other we use defer the transfer through a lambda function which knows the main alignment algorithm type.

rrahn avatar Jan 11 '21 19:01 rrahn

Codecov Report

Merging #2329 (26bba16) into master (77c5e8a) will decrease coverage by 0.03%. The diff coverage is 97.67%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2329      +/-   ##
==========================================
- Coverage   98.27%   98.23%   -0.04%     
==========================================
  Files         273      274       +1     
  Lines       10795    10836      +41     
==========================================
+ Hits        10609    10645      +36     
- Misses        186      191       +5     
Impacted Files Coverage Δ
...ise/detail/pairwise_alignment_algorithm_banded.hpp 100.00% <ø> (ø)
...rwise/detail/policy_alignment_algorithm_logger.hpp 96.29% <96.29%> (ø)
...qan3/alignment/pairwise/alignment_configurator.hpp 97.87% <100.00%> (+0.19%) :arrow_up:
...t/pairwise/detail/pairwise_alignment_algorithm.hpp 98.86% <100.00%> (+0.12%) :arrow_up:
...airwise/detail/policy_alignment_result_builder.hpp 100.00% <100.00%> (ø)
...atrix/detail/alignment_score_matrix_one_column.hpp 95.83% <0.00%> (-4.17%) :arrow_down:
...ment/matrix/detail/alignment_trace_matrix_full.hpp 96.77% <0.00%> (-3.23%) :arrow_down:
...gnment/pairwise/policy/alignment_matrix_policy.hpp 97.29% <0.00%> (-2.71%) :arrow_down:
.../seqan3/alignment/pairwise/alignment_algorithm.hpp 99.25% <0.00%> (-0.75%) :arrow_down:
... and 1 more

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codecov[bot] avatar Jan 11 '21 20:01 codecov[bot]

CodeCov is down because some parts of the old algorithm get not executed anymore.

rrahn avatar Jan 11 '21 22:01 rrahn

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vercel[bot] avatar May 11 '21 00:05 vercel[bot]

We will wait till Rene is back, he can reopen, or recreate a new PR

SGSSGene avatar Oct 18 '22 08:10 SGSSGene